?-Lytic protease, a serine protease, is specific for peptides containing a small hydrophobic side chain at the position just N-terminal to the hydrolyzed bond (the P1 position). Structural analysis of the reaction mechanism is possible by using transition state analogues, peptide inhibitors that form a covalent adduct between the P1 residue and the active site serine. Crystallographic studies in our lab show that amino acids in the substrate binding pocket adopt different conformations when bound to inhibitors with different P1 sidechains. i.e., a Met to Ala mutation (M190A) allows productive substrate binding for P1 sidechains as large as phenylalanine or as small as alanine, with the binding pocket swelling or shrinking to accommodate the change. We wish to study these conformational changes.